US6531581B1 - Purines and pyrimidines linked to a quencher - Google Patents
Purines and pyrimidines linked to a quencher Download PDFInfo
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- US6531581B1 US6531581B1 US09/646,669 US64666900A US6531581B1 US 6531581 B1 US6531581 B1 US 6531581B1 US 64666900 A US64666900 A US 64666900A US 6531581 B1 US6531581 B1 US 6531581B1
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
- C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
- C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
- C07H19/06—Pyrimidine radicals
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
- C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
- C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
- C07H19/06—Pyrimidine radicals
- C07H19/10—Pyrimidine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
- C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
- C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
- C07H19/16—Purine radicals
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
- C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
- C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
- C07H19/16—Purine radicals
- C07H19/20—Purine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
Definitions
- Radioisotope labeling includes the risk to the people handling the radioisotope-labeled material, and the need for elaborate and expensive safety precautions to be taken and maintained during the preparation, utilization and disposal of the radioactive material. Radioisotopes and radio-labeled nucleotides or polynucleotides are very expensive to purchase and use, due in part because of the safety precautions required and the problems in safely disposing of radioactive hazardous waste. In addition, the probe's structural integrity and sensitivity can be rapidly degraded during storage due to radioactive decay and radiochemical decomposition.
- Oligo and polynucleotides can also be labeled with biotin and iminobiotin, haptens and fluorescent dyes for the direct detection of nucleotides.
- biotin and iminobiotin haptens and fluorescent dyes for the direct detection of nucleotides.
- the hapten is detected by a labeled antibody and the biotin or iminobiotin is detected by a labeled avidin or strepavidin.
- the labeled nucleotides of Ruth are incorporated into oligo or polynucleotides by conventional phosphoramidite chemistry.
- the synthesized oligo or polynucleotides are then used as probes to detect DNA sequences. It is important to note that these labeled nucleotides are directly detectable when the probe is used in contrast to the labeled pyrimidines of the invention.
- FISH fluorescent in situ hybridization
- PCR has been adapted to use fluorescent molecules by incorporation of fluorescent labeled primers or nucleotides into the product which is then directly detected or by the use of fluorescent probes that are then detected. Removal of unincorporated, labeled substrates is usually necessary and can be accomplished by filtration, electrophoretic gel purification or chromatographic methods.
- electrophoretic gel purification or chromatographic methods the large amount of sample handling required by these analytical techniques make these purification methods labor intensive, not quantitative and they invariably leads to serious contamination problems.
- Affinity capture of PCR products by strepavidin coated beads or micro titer wells requires incorporation of biotin labels in addition to the fluorophores and still involves transfer steps that can lead to contamination.
- Instrumentation utilizing both gel electrophoresis and laser excitation optics represents an improvement in data acquisition but cannot handle large numbers of samples, retains the comparatively prolonged separation times characteristic of gels and still requires sample transfer.
- the unincorporated primer contains a target-specific, single stranded region with a 3′-hydroxyl terminus from which polymerase catalyzed elongation occurs.
- the unincorporated primer contains a tract of self complimentary nucleotides in the 5′ region that are hydrogen bonded into a hairpin conformation.
- the 5′-hydroxy terminus is modified with a fluorophore.
- the 5′-deoxynucleotide is adenosine (dA).
- the last base of the double stranded hairpin stem region is a deoxyuridine (dU) which is base paired to the 5′-dA.
- the aromatic azo dye 4-dimethylaminoazobenzene-4′-sulfonyl chloride (dabsyl) is linked via a spacer arm to the C-5 carbon of the dU base.
- Hairpins can be extremely stable structures for their size, having high Tm's and strongly negative free energies.
- a hairpin is an intramolecular formation and is much more kinetically and entropically favored than the formation of a hybridized duplex.
- the fluorophore and the DABSYL are tightly held in close proximity to each other. At these short molecular distances the fluorophore and DABSYL can have orbital contact and overlap, being able to form relatively weak chemical interactions such as it complexes, hydrogen bonding or salt complex formation.
- This orbital interaction promote very efficient transfer of excitation energy from the fluor to the dabsyl.
- the DABSYL acceptor is not fluorescent and dissipates much of the donated or transferred energy as heat. While resonance energy transfer plays a role in the fluorescein or other fluorophore quenching other mechanisms of energy transfer can operate over these short distances as well and can account for the very efficient quenching of the fluor by the quencher.
- the primer After target hybridization and polymerase extension, the primer becomes a template for the next round of DNA replication. Polymerase displaces the 5′-end of the hairpin and copies the remainder. This process opens the hairpin conformation and the primer enters into the standard double helical B DNA conformation. The fluorophore and DABSYL are then separated by more than 60 Angstroms. The incorporated primer is now capable of producing strong fluorescent emissions when exposed to the appropriate excitation wavelengths. Unincorporated primer remains as a hairpin and produces very little flourescent emission for the reasons previously stated.
- the hairpin, energy transfer primers are synthesized by standard automated phosphoramidite chemistry. See Caruthers, U.S. Pat. Nos.: 4,415,734 and 4,458,066 herein incorporated by reference. Linkage of the DABSYL moiety requires post synthetic modification.
- a commercially available dU phosphoramidite containing an aliphatic amino group linked to the base is incorporated. After deprotection and desalting the crude oligonucleotide is purified by reverse phase HPLC followed by solvent removal.
- the terminal amino group of the linker is reacted with a molar excess of commercially available dabsyl-succinimidyl ester or DABSYL sulfonyl chloride under alkaline conditions for 24 to 48 hours with the periodic addition of fresh, activated, dye during the incubation.
- the DABSYL modified oligonucleotide is precipitated and purified by reverse phase HPLC. After solvent removal the oligonucleotide is suspended in aqueous buffer, quantitated and tested.
- DABSYL coupling efficiencies are typically less than 80 percent and the entire process can take over a week to make preparative amounts of material. Final yields of product are typically much less than the coupling efficiency and are usually less than 50 percent.
- probes having a quencher incorporated by this method will have a greater background fluorescence than probes made from the quencher linked pyrimidines of the invention.
- the inventors have unexpectedly discovered that when mononucleotide precursors, in particular pyrimidines, are coupled to a quencher molecule and the quencher-pyrimidine is then incorporated into a probe using conventional phosphoramidite chemistry that the quencher-pyrimidine is stable during the protection and deprotection steps and is itself incorporated in good yield during the synthesis of hairpin, energy-transfer primers.
- the overall synthesis of the primers is also not effected by the quencher-pyrimidine nucleotide.
- the fluorophore will act as a fluorescence indicator when the hairpin is unfolded because the distance between the quencher and the fluorophore is greatly increased.
- L is a linker group, preferably comprising at least three carbon atoms, and Q is a quencher group;
- P is a pyrimidine group, preferably a uracil or cytosine group, and L is linked to the carbon atom at the 4 or 5 position of P, or P is a purine group, preferably an adenine group, and L is directly or indirectly linked to the carbon at the 8 position of P;
- x is an activated phosphorous group capable of bonding to a 3′ hydroxyl group of another nucleotide, y is a protected hydroxyl group, and z is —H, —F, —OCH 3 , —O—allyl, a protected hydroxyl group, or a protected amine group, or y is an activated phosphorous group capable of bonding to a 5′ hydroxyl group of another nucleotide, x is a protected hydroxyl group, and z is —H, —F, —OC
- the linker has the following structure: —CH ⁇ CH—C(O)—NH—(CH 2 ) n —NH—, —CH ⁇ CH—C(O)—NH—CH 2 —CH 2 —(O—CH 2 —CH 2 ) m —NH—, —C ⁇ C—C(O)—(CH 2 ) n —NH—, —CH ⁇ CH—C(O)—NH—(CH 2 ) n —CO 2 —, —CH ⁇ CH—C(O)—NH—(CH 2 ) n —NH—, —(CH 2 ) n —NH—, or —NH—(CH 2 ) n —NH—, wherein n is an integer from 2 to 12, and m is 1 or 2.
- the linker has the following structure: —CH ⁇ CH—C(O)—NH—(CH 2 ) 6 —NH—, —(CH 2 ) 3 —NH—, or —NH—(CH 2 ) 3 —NH—.
- Q is a quencher capable of quenching the fluorescence of a flourescent dye when the quencher and dye are incorporated into a hairpin oligonucleotide.
- the quencher is capable of substantially suppressing the fluorescence of the flourescent dye until the oligonucleotide is fully unfolded and is not in the hairpin conformation.
- x, y, and z each are —H, HO—, HO—P( ⁇ O)(—OH)—O—, HOP( ⁇ O)(—OH)—O—P( ⁇ O)(—OH)—O—, HOP( ⁇ O)(—OH)—O—P( ⁇ O)(—OH)—O—P( ⁇ O)(—OH)—O—, —OCH 3 , —F, —NH 2 , —O—allyl, benzyl, dimethoxytrityl, trityl, acetyl, phosphothioate such as is (HO) 2 P( ⁇ S)—O— or (HO) 2 —P( ⁇ O)—O—(HO)P( ⁇ O)—O—(HO)P( ⁇ S)—O—, methyl phosphoamidite, methyl Dhosphonoamidite, H-phosphonate, phosphotriester, —O-propargyl, silyl, and phosphoami
- the quencher is preferably a non-fluorescent dye, e.g., acid alizarin violet N, acid black 24, acid blue 29, acid blue 92, acid blue 113, acid blue 120, and blue 161, acid orange 8, acid orange 51, acid orange 74, acid red 1, acid red 4, acid red 8, acid red 37, acid red 40, acid red 88, acid red 97, acid red 106, acid red 151, acid red 183, acid violet 7, acid yellow 17, acid yellow 25, acid yellow 29, acid yellow 34, acid yellow 38, acid yellow 40, acid yellow 42, acid yellow 65, acid yellow 76, acid yellow 99, alizarin yellow 66, crocein orange G, alizarin blue black B, palatine chrome black 6BN, mordant black 3, basic red 29, basic blue 66, brilliant yellow chrysophine, chrysoldin, crocein orange G, crystal scarlet, fast black K salt, fast corinth V salt, fast garnet GBC, fat brown B, fat brown RR, mordant blue 9, mordant brown 1,
- the non-fluorescent triphenyl methane dye contains an isocyanate group, an isothiocyanate group, or an N-succinimidyl ester group.
- the quencher is malachite green, it preferably contains an amine group bonded to the atom at the 4 position.
- Other preferred quenchers are uniblue B, alizarin blue black B, alizarin red S, alizarin violet 3R, fast blue BB, and fast blue RR.
- the quencher has the following general structure (B):
- T is —NH—, —SO 2 —, —O—, —S—, —C(O)—S—, —C(O)—, —C(O)—NH—, —C(O)—O—, —C(S)—NH—, or —C(S)—O—;
- a, a′, b, b′, c, c′, d, d′, and e′ are each —H, —Cl, —Br, —F, —OCH 3 , —OH, —CH 3 , —SO 3 —, diazophenyl, diazo-1-naphthyl, —CO 2 R, or —N(R) 2 ; and R is —H, —CH 3 , —CH 2 —CH 3 , or O.
- the invention is also directed to a method for producing a compound containing at least two nucleotide groups, e.g., an oligonucleotide, wherein the method comprises linking the compound of claim 1 to another compound containing at least one nucleotide or nucleotide group.
- the compounds of the invention can be readily prepared by the following process:
- a quencher selected from non-fluorescent azo dyes and non-fluorescent triphenyl methane dyes and other suitable compounds having at least one moiety capable of reacting with the amino functionality of the Pyr-L-NH 2 preferably with a quencher having a sulfonyl chloride, carboxylic acid chloride, N-succinimidyl ester, isocyanate or isothiocyanate.
- the terminal —NH 2 group of the linker is activated by forming an isocyanate or isothiocyanate and then reacting the isocyanate or isothiocyanate with an alcohol or amino moiety on the dye to form the desired pyrimidine-quencher compound.
- the P-L-quencher described above is then used in the preparation of primers.
- the P-L-quencher are readily incorporated into the growing oligonucleotide during its synthesis using automated oligonucleotide techniques and equipment.
- DABSYL was a preferred quencher.
- DABSYL or other quenchers are not available in the form of dabsyl-nucleotide phosphoamidites. Consequently, a deoxyuridine ⁇ -cyanoethyl phosphoramidite containing a DABSYL moiety linked to the base via a linker arm (dU-dabsyl) was prepared as described in the present application.
- a number of hairpin primers incorporating a pyrimidine-quencher were synthesized on an automatic DNA synthesizer.
- Analytical HPLC revealed an increase in primer yields to between 80 to 90%, indicating surprisingly efficient coupling of the dU-DABSYL and stability of the dU-DABSYL through many synthetic cycles.
- Analysis of the fluorescent properties of these primers revealed unexpectedly high signal to noise ratios in samples that had only been desalted and not purified by HPLC.
- the enhanced signal to noise in impure samples may be due to the incorporation of the DABSYL before the addition of the fluorophore because the synthesis of oligonucleotides occur in the 3′ to 5′ direction.
- FIG. 1 is a graph plotting fluorescence versus the number of PCR cycles for differing concentrations of recombinant HIV 1 DNA.
- the present invention provides a quencher moiety attached by a linker arm to a purine or pyrimidine nucleotide having the following structure (A):
- the quencher-linker-P nucleotide can be readily incorporated into oligonucleotides using conventional solid phase oligonucleotide synthetic techniques described by Caruthers et al. in U.S. Pat. Nos. 4,415,734 and 4,458,066 or by techniques of Letsinger et al. J. Org. Chem. vol. 45, 2715 (1980) and reviewed by Matteuci et al. J. Amer. Chem. Soc.: vol. 103 p. 3185 (1982) both articles herein incorporated by reference.
- Preferred oligonucleotides with the quencher-P are hairpin probes with a flourescent dye at the 5′-end of the oligonucleotide as described in Nucleic Acid Amplification of Oligonucleotides with Molecular Energy Transfer Labels and Methods Based , U.S. Pat. No. 5,866,336.
- the quencher and the flourescent dye are in close proximity to each other so that the quencher will quench the fluorescence of the fluorescent dye and when the oligonucleotide is in the linear configuration the quencher and fluorescent dye are far enough apart so that the quencher no longer quenches the fluorescence of the fluorescent dye.
- preferred quenchers are non-fluorescent azo dyes, non-fluorescent triphenyl methane dyes, and dyes such as Uniblue-B.
- the dyes should be non-fluorescent because an acceptor fluorescent dye can have fluorescent emissions that will spill into assay wavelengths and increase the background noise.
- emissions from fluorescent quenchers can interfere with applications involving several different assay fluorophores having different colors. Examples of such applications would include multiplex PCR and fluorescent internal controls.
- Preferred non-flourescent azo dyes have the following structure (B):
- T is independently selected from —NH—, —SO 2 —, —O—, —S—, —(CO)—S—, —C(O), C(O)—NH—, —C(O)—O—, —C(S)—NH— and —C(S)—O—;
- a, a′, b, b′, c, c′, d, d′ and e′ are independently selected from H, Cl, Br, F, —OCH 3 , —OH, —CH 3 , —SO 3 —, diazophenyl, diazo-1-naphthyl, —CO 2 R and N(R) 2 and R is independently selected from H, —CH 3 , —CH 2 —, —CH 3 and O.
- Particularly preferred compounds are those where e′ is —N(R) 2 and R is independently selected from H, —CH 3 and —CH 2 CH 3 . Even more preferred are nonflourescent azo dyes when a, a′, b, b′, c, c′, d and d′ are H, and e′ is N(R) 2 wherein R is —CH 3 or —CH 2 CH 3 , and T is SO 2 .
- non-fluorescent azo dyes which may be used according to the invention are as follows: acid alizarin violet N, acid black 24, acid blue 29, acid blue 92, acid blue 113, acid blue 120, acid blue 161, acid orange 8, acid orange 51, acid orange 74, acid red 1, acid red 4, acid red 8, acid red 37, acid red 40, acid red 88, acid red 97, acid red 106, acid red 151, acid red 183, acid violet 5, acid violet 7, acid yellow 17, acid yellow 25, acid yellow 29, acid yellow 34, acid yellow 38, acid yellow 40, acid yellow 42, acid yellow 65, acid yellow 76, acid yellow 99, alizarin yellow 66, alizarin blue, black B, palatine chrome black 6BN, mordant black 3, basic red 29, basic blue 66, brilliant yellow chrysophenine, chrysoldin, crocein orange G, crystal scarlet, fast black K salt, fast corinth V salt, fast garnet GBC, fat brown B, fat brown RR, mordant blue 9, mordant brown 1, mord
- non-flourescent azo dyes include acid aldzarin violet N, acid black 24, acid blue 92, acid blue 113, acid blue 120, acid orange 8, acid orange 51, acid orange 74, acid red 1, acid red 4, acid red 8, acid red 37, acid red 88, acid red 151, acid red 183, acid yellow 34, acid yellow 40, acid yellow 76, crocein orange G, crystal scarlet, mordant blue 9, mordant brown 1, mordant brown 33, mordant orange 1, mordant orange 6, mordant orange 10, orange 11, orange G, palatine chrome black 6BN, palatine fast yellow BLN and topaeolin O.
- non-fluorescent triphenyl methane dyes which can be used according to the invention are selected from: alkali blue 6B, aniline blue, aurintricarboxylic acid, basic violet 14, basic red 9, brilliant green, bromochlorophenol blue, bromocresol purple, chlorophenol red, m-cresol purple, cresol red, crystal violet, ethyl violet, fast green FCF, guinea green B, malachite green, methyl green, new fuschia, pyrocatechol violet, thymol blue, thymolphthalein, victoria blue B, victoria blue R and victoria pure blue, both as the isocyanate or isothiocyanate derivatives.
- a preferred non-fluorescent triphenyl methane dye is malachite green derivatized at the 4 position of the phenyl ring with isothiocyanate.
- Other non-fluorescent dyes that can be used as a quencher include alizarin blue black B, alizarin red S, alizarin violet 3R, fast blue BB, and fast blue RR.
- the concentration of the hairpin probe in an assay system is such that the non-fluorescent dye is not detectable by a spectrophotometer.
- pyrimidines which can be used are uridine, thymadine, and cytosine. Uridine is preferred.
- the linker, L comprises at least three carbon atoms and links the pyrimidine with the quencher moieties.
- Preferred examples of the linker, L, which can be used in the invention are:
- the preferred linkers are —CH ⁇ CH—C(O)—NH—(CH 2 ) n —NH— and —CH ⁇ CH—C(O)—NH—CH 2 —CH 2 —(O—CH 2 —CH 2 ) m —NH— and n is 2-12 and m is 1, 2 or 3.
- Each of x, y and z are selected as follows: whenever x is an activated phosphorus group capable of intermolecular bond formation with a 3′ hydroxyl of another nucleotide, then y is a protected hydroxyl group and z is —H, —F, —OCH 3 , —O-allyl or a protected hydroxyl or amine group and whenever y is an activated phosphorus group capable of intermolecular bond formation with a 5′ hydroxyl of another nucleotide then x is a protected hydroxyl group and z is —H, —F, —OCH 3 , —O-allyl or a protected hydroxyl or amine group.
- Preferred x, y and z's are selected from —H, HO—, HO—P( ⁇ O)(—OH)—O—, HOP( ⁇ O)(—OH)—O—P( ⁇ O)(—OH)—O—, HOP( ⁇ O)(—OH)—O—P( ⁇ O)(—OH)—O—P( ⁇ O)(—OH)—O—, —OCH 3 , —F, —NH 2 , —O-allyl, benzyl, dimethoxytrityl, trityl, acetyl, phosphothioates such as (HO) 2 P( ⁇ S)—O—, (HO) 2 P( ⁇ O)—O—(HO)P( ⁇ O)—O—(HO)P( ⁇ S)—O—, methyl phosphoamidite, methyl phosphonoamidite, H-phosphonate, phosphotriesters, —O-propargyl, silyls, support bound such as
- the protective group for hydroxyl compounds is a —O-silyl group
- the silyl group is selected from the group consisting of trimethylsilyl, triisopropylsilyl and t-butyldimethylsilyl.
- the quencher molecule may have a sulfonic acid or carboxylic acid moiety which is derivatized to the corresponding acid chloride.
- the acid chloride moiety of the quencher molecule is allowed to react with the amino moiety of the linker group to form the corresponding amide.
- the quencher molecule may have an amine or hydroxy moiety which is attached to the amine group of the linker arm by either derivatizing the amine group of the linker to form an isocyanate or isothiocyanate and then allowing the isocyanate or isothiocyanate group of the linker to react with the amine or hydroxyl group of the quencher molecule to form the respective urea or thiourea and carbamate or thiocarbamate groups.
- the amine group of the quencher can also be derivatized to form the isocyanate or isothiocyanate and allowed to react with the amine group of the linker to again form the urea or thiourea link.
- the hydroxy group can be derivatized to form the chlorocarbonate which is allowed to react with the amine group to form the respective carbamate.
- the terminal group of the linker is a carboxylic acid the carboxylic acid can be reacted with alcohols or arnines on the quencher to form the respective esters and amides with the quencher.
- the amine of the linker group can be allowed to react with the aldehyde, followed by reduction of the imine with sodium cyanoborohydride or other reducing agents to form an amine linkage.
- Another, alternative method of making the quencher-pyrimidines of the invention is to react the amine functionality of the linker group with the quencher before the linker arm is attached to the nucleotide to form a linker-quencher.
- This reaction between the linker and quencher can be accomplished by a variety of different, conventional, organic reactions such as the reaction of acid chlorides or acid anhydrides with amines to form amides.
- the reactions can include, depending on the terminal group of the linker and the quencher, the reaction of a sulfonyl chloride with an amine to form a sulfonamide, the reaction of an isocyanate with an amine or alcohol to form a urea or a carbamate respectively, the reaction of an isothiocyanate with an amine or alcohol to form a thiourea or thiocarbamate respectively or the reaction of an activated carboxylic acid with an alcohol or amine to form an ester or amide, respectively.
- the nucleotides-quencher molecules of the invention can be readily incorporated into oligo and polynucleotides using conventional phosphoramidite chemistry.
- the quencher molecule even though it is a dye molecule as described in this application, is undetectable spectrophotometrically, when the probes are used at a concentration suitable for polynucleotide amplification.
- TFA trifluoroacetyl protecting group
- derivatized ethyl orange can be added to the pyrimidine-nucleotide to which the linker has been incorporated in place of the DABSYL chloride.
- ethyl orange is derivatized to the corresponding sulfonyl chloride.
- a compound of Formula (C) 1 eq.
- 2 eq. of phosphorus pentachloride in solution is added drop-wise.
- the reaction mixture is heated and upon completion of the reaction, the reaction mix is poured over ice, the product is collected by suction filtration. The dry product is washed with acetone in an extractor.
- the ethyl orange can also be derivatized by reaction with thionyl chloride as follows. To a round bottom flask fitted with a reflux condensor and a magnetic stirrer containing 1 eq. of ethyl orange is added 5 eq. of thionyl chloride drop-wise. The reaction mixture is heated and stirred until the reaction is complete. Excess thionyl chloride is driven off by distillation under reduced pressure and the derivatized product is recovered.
- naphthyl red, fast garnet GBC or 4-phenylazoaniline can be used in place of the DABSYL chloride.
- sodium nitrite is added in excess with concentrated HCl in an ice bath (0° C.) to the dye to yield a non-isolated intermediate of a diazonoium salt of the dye.
- the intermediate is subsequently reacted with SO 2 , CuCl 2 and KCl in a suitable solvent system, e.g., a 1:1 mixture of benzene and dioxane. The mixture is heated to about 50° C., for about at least 30 minutes.
- reaction is quenched with the addition of water, and the product is extracted with a solvent.
- product is then washed with an aqueous solution of NaOH, extracted again with a suitable solvent and then the solvent is removed by, e.g., rotary evaporator and dried over, e.g., Celite®.
- fast corinth V can be used in place of DABSYL chloride, but is derivatized to its sulfonyl chloride prior to incorporation in the pyrimidine-nucleoside.
- Fast corinth V has the following structure:
- Fast corinth V is reacted with SO 2 , CuCl 2 and KCl in a suitable solvent system, e.g., a 1:1 mixture of benzene and dioxane.
- a suitable solvent system e.g., a 1:1 mixture of benzene and dioxane.
- the mixture is heated to about 50° C., for about at least 30 minutes.
- the reaction is quenched by the addition of water, and the product is extracted with a solvent.
- the product is then washed with an aqueous solution of NaOH, extracted again with a suitable solvent and then the solvent is removed by, e.g., rotary evaporator and dried over a drying agent, e.g., Celite®.
- dyes such as naphthyl red, fast garnet and 4-phenylazoaniline can be derivatized to their corresponding isothiocyanates or succinimidyl esters as detailed below.
- the isothiocyanate of any of the above dyes is prepared by combining the dye with an excess of thiocarbonyldiimidazole to yield the isothiocyanate of the dye.
- the isothiocyanates of naphthyl red, fast garnet GBC and 4-phenylazoaniline are as follows:
- the isothiocyanates can be prepared by reacting the dye with thiophosgene with a solvent, such as pyridine or triethylamine with heating from 0° to 50° C. The excess reagent is removed by distillation under reduced pressure and the product is then recovered.
- a solvent such as pyridine or triethylamine
- succinimidyl esters such as the succinimidyl ester of ethyl red
- the succinimidyl esters is prepared by reacting the dye with N-hydroxysuccinimide and DCC (dicyclohexylcarbodiimide) in a DMF (dimethylformamide) solvent system at about 0° for about 10 to 20 hours.
- DCC diclohexylcarbodiimide
- DMF dimethylformamide
- the structure and sequence of the oligonucleotide can have large effects on the quench values.
- Oligonucleotides containing a dU linked amino group, similar to V of Example 1 were derivatized with malachite green isothiocyanate and purified by HPLC. Fluorescence assays using oligonucleotides similar to the oligonucleotides of Example 2 were performed and the results shown in Table 2 were obtained:
- the structure and sequence of the oligonucleotides can have large effects on the quench values.
- oligonucleotide primers were chemically synthesized and purified:
- BSK 38 was synthesized using phosphoramidite chemistry with standard cycles at 0.2 ⁇ mol scale on an Applied Biosystems-PE 394 synthesizer.
- the oligonucleotide was cleaved from the support and deprotected in ammonium hydroxide at 55° C. for 10 hours. Ammonium hydroxide and low molecular weight contaminants were removed by gel filtration chromatography on Sephadex G-25. The column was equilibrated and eluted with deionized water.
- the primer was quantitated by UV spectroscopy at 260 nm and has the following sequence: d(ATAATCCACCCTATCCCAGTAGGAGAAAT) (SEQ ID NO: 1).
- BSK 39 was synthesized by phosphoramidite chemistry on an Applied Biosystems-PE 394 synthesizer at a 1.0 ⁇ mol scale. Standard base coupling steps and acetylation times were extended to one minute and 10 seconds respectively. Prior to synthesis 50 ⁇ mol of dry dU-DABSYL phosphoramidite was dissolved in anhydrous acetonitrile at a concentration of 100 mM. At the appropriate step the dU DABSYL was allowed to couple for ten minutes. The 5′ terminus of the oligonucleotide was labeled by the addition of a fluorescein phosphoramidite at the terminal step.
- the oligonucleotide was deprotected at room temperature for 24 hours in ammonium hydroxide. Ammonium hydroxide and low molecular weight contaminants were removed by gel filtration chromatography on Sephadex G-25. The column was equilibrated and eluted with deionized water. The oligonucleotide was further purified by reverse phase HPLC. After solvent removal the oligonucleotide was dissolved in deionized water and quantitated by UV spectrophotometry. The signal to noise values were determined in a Shimadzu spectrofluorimeter using excitation and emission wavelengths of 495 and 516 nm respectively.
- the fluorescence of 5 pmol of oligonucleotide was determined in 0.6 ml of 10 mM Tris-HCl pH 8.0, 2 mM MgCl 2 , 50 mM NaCl or 15 mM NaOH. A 30-fold difference in fluorescence was observed between reading taken in neutral buffers (hairpin conformation) and alkaline solutions (linear conformations). Over a 20-fold increase in fluorescence is observed in neutral buffers when an excess of complimentary oligonucleotide target is added.
- the BSK 39 has the following sequence: d((Fluoroscein)ACCGCTGCGTGAGCAGCGGU(dabsyl)CCTTGTCTTAGTCCAGAA) (SEQ ID NO:2).
- the PCR reaction between the BSK 38 and BSK 39 primers and cloned HIV 1 control DNA was performed and monitored in an Idaho Lightcycler, Idaho Instruments Inc. Idaho Falls, Id.
- the reaction mixture of 20 mM Tris (ph 8.4), 50 mM KCl, 3 mM MgCl 2 0.5 mg per mole bovine serum albumin (BSA) and 0.2 mM dNTP was added to 0.25 ⁇ M BSK 38 and 0.25 ⁇ M BSK 39 with 0.5 units of Taq (Takara) per 10 ⁇ l and 10 to 10 6 molecules of cloned HIV 1 control DNA.
- the reaction was set up by diluting the DNA polymerase 10 times with Idaho dilution buffer (10 mM Tris (pH 8.4) and 2.5 mg per ml BSA) to a concentration of 0.5 units per ⁇ l.
- the reaction cocktail was made with 0.25 mg/ml of BSA (final) and one half of the BSA was coming from the cocktail and one half from the DNA polymerase solution.
- the capillary tubes were filled as described in the Idaho Lightcycler manual. Cycling conditions of 4 minutes at 94 followed by 1 second at 94 then 15 seconds at 55 and 40 seconds at 74 before repeating the cycle.
- diaminopropane is added along with NaHSO 3 in water at a pH of about 7.1 at 37° C. for about 5 to 7 days.
- the compound of formula (XI) is purified on a silica gel column with an eluant comprising 5-20% of ethyl acetate in methanol. Upon purification, the alcohol of the methanol moiety is protected by reacting the compound of formula (XI) with dimethoxytrityl chloride with triethylamine and pyridine to yield the compound of formula (XII).
- the alcohol protected compound is purified by dissolving in methanol, vacuum drying and purifying on a silica gel column with an CHCl 3 /methanol eluting system.
- the purified protected compound is reacted with methylamine in methanol at about 40° C. and subsequently dried to yield the compound of formula (XIII).
- the compound of formula (XIII) can be reacted with any number of Q groups such as the succinimidyl esters, isothiocyanates, or sulfonyl chlorides such as DABSYL sulfonyl chloride, followed by subsequent conversion of the free hydroxyl to a phospohoramidate to yield a compound of formula (XIV):
- liquid bromine with water is added along with sodium acetate in water at a pH of about 5.0.
- the reaction mixture is heated until the reaction was complete and the compound of formula (XVI) is formed.
- the compound of formula XVI is taken up in pyridine and cooled to 0° C. Trimethylchlorosilane is added drop-wise, followed by addition of benzylchloride. Following the addition of benzylchloride, water and NH 3 are added. The reaction mixture is dried and the product is extracted with ether. The compound of formula (XVII) is yielded.
- the alcohol of the methanol moiety is protected by reacting the compound of formula (XVII) with dimethoxytrityl chloride with triethylamine and pyridine to yield the compound of formula (XVIII).
- the compound is washed with sodium bicarbonate and purified by silica gel column chromatography.
- the compound of formula (XVII)) is refluxed with ethanol and diaminopropane and purified on a silica gel column to yield the compound of formula (XIX).
- the protected alcohol can be reacted with any number of Q groups, for example DABSYL sulfonyl chloride in triethylamine and DMF, to yield the compound of formula (XX).
Abstract
Description
TABLE 1 | ||||
Fluorophore | Excitation/Emission (nm) | Fold Quench | ||
AMCA | 353/450 | 15 | ||
Fluorescein | 495/516 | 52 | ||
JOE | 535/555 | 50 | ||
TAMRA | 560/584 | 37 | ||
Bodipy 564 | 580/590 | 15 | ||
ROX | 594/616 | 23 | ||
Texas Red | 595/620 | 18 | ||
TABLE 2 | ||||
Fluorophore | Excitation/Emission (nm) | Fold Quench | ||
TAMRA | 560/584 | 3.0 | ||
ROX | 594/616 | 3.5 | ||
Bodipy 581 | 590/605 | 4.0 | ||
Texas Red | 595/620 | 5.0 | ||
Claims (20)
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PCT/US1999/013107 WO1999064431A2 (en) | 1998-06-10 | 1999-06-10 | Purines and pyrimidines linked to a quencher |
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Also Published As
Publication number | Publication date |
---|---|
US6117986A (en) | 2000-09-12 |
EP1086115A2 (en) | 2001-03-28 |
JP2002517505A (en) | 2002-06-18 |
WO1999064431A3 (en) | 2000-06-15 |
CA2334610A1 (en) | 1999-12-16 |
WO1999064431A2 (en) | 1999-12-16 |
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